chloro SSR data

Genetic data obtained for the six chloroplast microsatellite loci ccmp2 (or ibcp4), ntcp28 (or ibcp31), ibcp5, ibcp10, ibcp8 and ntcp26 for herbarium specimens (57 specimens in total; sheet 1) and samples collected in ex situ collections (in total 1153 samples; sheet 2). Passeport data of all accessions are provided along genetic results: - for herbarium specimens, it includes herbarium codes, geographical origin, dates of collection, collector names along with genetic data, ie, allele code for each locus, haplotype code and cp lineage (1 or 2). - for ex situ samples, it includes names of ex situ collections, full geographical origin data and local landrace names, along with genetic data, ie, allele code for each locus, haplotype code and cp lineage (1 or 2)Genetic data obtained for the six chloroplast microsatellite loci ccmp2 (or ibcp4), ntcp28 (or ibcp31), ibcp5, ibcp10, ibcp8 and ntcp26 for herbarium specimens (57 specimens in total; sheet 1) and samples collected in ex situ collections (in total 1153 samples; sheet 2). Passeport data of all accessions are provided along genetic results: - for herbarium specimens, it includes herbarium codes, geographical origin, dates of collection, collector names along with genetic data, ie, allele code for each locus, haplotype code and cp lineage (1 or 2). - for ex situ samples, it includes names of ex situ collections, full geographical origin data and local landrace names, along with genetic data, ie, allele code for each locus, haplotype code and cp lineage (1 or 2)

DRYAD Sample Location

Passeport data of the 334 accessions used in the present manuscript. Accession CIP number, accession name, Collection number, Accession country of origin, Elevation of collecting site, Latitude and Longitude of collecting site, are provided. All accessions are issued from CIP genebank (International potato center). Complete passeport data are also available on the CIP web site (http://germplasmdb.cip.cgiar.org/biomart/martview/acc7fbd28f3343fa2c81be86a979e5a3)

cpSSRs data

Choloroplast microsatellites data. Each accession number is presented with its allelic composition for the seven loci used in our study (ccmp2, ntcp18, ntcp28, ntcp26, ibcp5, ibcp8 and ibcp10)

nuclear SSRs data

Nuclear microsatellites data of the 130 New World sweet potato landraces. For hexaploids, we can obtain from 1 to 6 peaks or bands (6 alleles) per locus. Allelic composition (from allele 1 to allele 6) is provided for each accession, for the 13 microsatellites used in our study

Two possible scenarios about the origins of <i>Ipomoea batatas.</i>

<p>a) Scenario A which represents according to us, the most parsimonious scenario explaining the clear-cut phylogeographical pattern inferred from both nuclear and chloroplast data: 1) Multiple independent events of autopolypoidy within several polymorphic and pre-differentiated wild populations (phylogeographical differentiation), and then 2) multi-local domestication within each polyploid population, followed by 3) gene flow between the two cultivated genepools and between cultivated and wild forms. b) Scenario B: 1) Hybridization between differentiated conspecific wild populations (in contact because of potential climate-induced or human-induced range shift) and polyploidization, followed by 2) the domestication of these polyploids forms and then 3) patterns of post-domestication human expansion may have been responsible for the clear-cut phylogeographical pattern found within cultivated <i>I. batatas</i> in tropical America. Finally, 4) Gene flow between the two cultivated genepools and between cultivated and wild forms may also have occurred.</p

Sampling geographical distribution.

<p>Location of <i>I. triloba</i>, <i>I. trifida</i>, <i>I. batatas</i> and polyploid <i>Ipomoea</i> sp. accessions used in the present study and current taxon distribution ranges, as determined from GBIF records (<a href="http://data.gbif.org/species/" target="_blank">http://data.gbif.org/species/</a>) are provided. Accessions with no geographical information are not shown; details on sampling are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062707#pone.0062707.s005" target="_blank">Tables S1</a>.</p

Contingency table comparing cpDNA haplotype “lineages” with DAPC clusters among the different taxa <i>I. batatas</i>, <i>I. trifida</i>, <i>I. triloba</i>, <i>Ipomoea</i> sp. (including <i>I. tabascana</i>).

<p><i>I. trifida</i> haplotypes correspond to hap2, 5, 9, 10, 14, 15, 16, 17 and <i>I. triloba</i> haplotypes to hap3, 8 and 18.</p

Genetic relationships of <i>I. batatas</i>, five wild relatives and <i>Ipomoea</i> sp. accessions based on chloroplast DNA analyses.

<p>Statistical Parsimony Network of rpl32-trnL(UAG) haplotypes. Circle size is proportional to the number of individuals per haplotype. Substitutions and inversions are represented using full lines and indels are displayed using broken lines. Intermediate, unsampled haplotypes appear as dots. The posterior probability of two nodes, as obtained through a Bayesian tree reconstruction (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062707#pone.0062707.s001" target="_blank">Figure S1</a>), is reported in italics. The ploidy level of <i>Ipomoea</i> sp. accessions is indicated.</p

Taxa boundaries as accessed with DAPC analysis for nuclear SSR data.

<p>Diagram representing the proportion of membership probabilities in nuclear five clusters (K1, K2, K3, K4 and K5) as determined by the DAPC analysis. Each individual is represented as a vertical bar, with colours corresponding to membership probabilities to the five clusters.</p

Genetic diversity of the four geographically well-sampled taxa as revealed by nuclear SSRs.

<p>Values for the number of alleles (<i>NA</i>), its rarefied value over 25 individuals (1000 resamplings; <i>Ar</i>) and the observed and expected heterozygosities <i>Ho</i> and <i>He</i>, are provided both per locus and as mean values averaged over all loci. <i>D</i> corresponds to the intra-taxon mean Lynch distance between genotypes.</p